+Open data
-Basic information
Entry | Database: PDB / ID: 3j7q | |||||||||||||||
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Title | Structure of the idle mammalian ribosome-Sec61 complex | |||||||||||||||
Components |
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Keywords | RIBOSOME / mammalian / Sec61 / translocation / translation | |||||||||||||||
Function / homology | Function and homology information : / regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...: / regulation of cell cycle => GO:0051726 / regulation of cell cycle => GO:0051726 / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-transporting ATPase activity / embryonic brain development / translation at presynapse / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / organelle membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein localization to nucleus / protein-RNA complex assembly / protein targeting / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / rRNA processing / protein tag activity / large ribosomal subunit / protein transport / ribosome biogenesis / presynapse / regulation of translation / heparin binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / membrane => GO:0016020 / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / glutamatergic synapse / synapse / positive regulation of gene expression / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa (pig) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Voorhees, R.M. / Fernandez, I.S. / Scheres, S.H.W. / Hegde, R.S. | |||||||||||||||
Citation | Journal: Cell / Year: 2014 Title: Structure of the mammalian ribosome-Sec61 complex to 3.4 Å resolution. Authors: Rebecca M Voorhees / Israel S Fernández / Sjors H W Scheres / Ramanujan S Hegde / Abstract: Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either ...Cotranslational protein translocation is a universally conserved process for secretory and membrane protein biosynthesis. Nascent polypeptides emerging from a translating ribosome are either transported across or inserted into the membrane via the ribosome-bound Sec61 channel. Here, we report structures of a mammalian ribosome-Sec61 complex in both idle and translating states, determined to 3.4 and 3.9 Å resolution. The data sets permit building of a near-complete atomic model of the mammalian ribosome, visualization of A/P and P/E hybrid-state tRNAs, and analysis of a nascent polypeptide in the exit tunnel. Unprecedented chemical detail is observed for both the ribosome-Sec61 interaction and the conformational state of Sec61 upon ribosome binding. Comparison of the maps from idle and translating complexes suggests how conformational changes to the Sec61 channel could facilitate translocation of a secreted polypeptide. The high-resolution structure of the mammalian ribosome-Sec61 complex provides a valuable reference for future functional and structural studies. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j7q.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j7q.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3j7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j7q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3j7q_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3j7q_validation.xml.gz | 234.2 KB | Display | |
Data in CIF | 3j7q_validation.cif.gz | 397.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/3j7q ftp://data.pdbj.org/pub/pdb/validation_reports/j7/3j7q | HTTPS FTP |
-Related structure data
Related structure data | 2650MC 2644C 2646C 2649C 3j7oC 3j7pC 3j7rC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules 578
#1: RNA chain | Mass: 1206101.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
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#2: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 371913672 |
#3: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: GenBank: 115552481 |
+Ribosomal protein ... , 42 types, 42 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-Protein , 2 types, 2 molecules 12
#46: Protein | Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480EHF8 |
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#47: Protein | Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas / References: UniProt: A0A480WFL1 |
-Protein/peptide , 1 types, 1 molecules 3
#48: Protein/peptide | Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: pancreas |
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-Non-polymers , 2 types, 133 molecules
#49: Chemical | ChemComp-MG / #50: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The ribosome-Sec61 complex purified from porcine pancreas Type: RIBOSOME |
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Buffer solution | Name: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin pH: 7.5 Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil R2/2 400 mesh copper grids |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 120 K Details: 3 uL sample was incubated on the grid for 30 seconds and blotted for 9 seconds before being plunged into liquid ethane (FEI VITROBOT MARK IV). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 7, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder type: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Details: Back-thinned |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each particle | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: Single particle / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80019 / Nominal pixel size: 1.34 Å / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 37 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor and FSC / Details: METHOD--Maximum likelihood | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 3.5→268 Å / Cor.coef. Fo:Fc: 0.856 / SU B: 22.493 / SU ML: 0.34 / σ(F): 0 / ESU R: 0.873 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.35 Å2 / Biso mean: 48.645 Å2 / Biso min: 14.64 Å2
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.591 Å / Total num. of bins used: 20
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